Zinc in PDB 1qtw: High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV

All present enzymatic activity of High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV:
3.1.21.2;

The structure of High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV, PDB code: 1qtw was solved by D.J.Hosfield, Y.Guan, B.J.Haas, R.P.Cunningham, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.620, 59.560, 50.980, 90.00, 110.94, 90.00
R / Rfree (%)	12.4 / 14.8

The binding sites of Zinc atom in the High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV (pdb code 1qtw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV, PDB code: 1qtw:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.3 occ:1.00 O A:HOH1001 1.9 7.7 1.0 NE2 A:HIS109 2.0 8.2 1.0 NE2 A:HIS69 2.0 8.0 1.0 OE2 A:GLU145 2.1 7.7 1.0 CD2 A:HIS109 2.9 8.5 1.0 CD A:GLU145 2.9 7.1 1.0 CE1 A:HIS69 3.0 8.5 1.0 HD2 A:HIS109 3.0 10.2 1.0 CE1 A:HIS109 3.1 9.8 1.0 CD2 A:HIS69 3.1 7.9 1.0 OE1 A:GLU145 3.1 7.7 1.0 HE1 A:HIS69 3.2 10.2 1.0 HD2 A:HIS69 3.3 9.4 1.0 HE1 A:HIS109 3.3 11.7 1.0 HD22 A:ASN107 3.4 11.0 1.0 HE1 A:HIS216 3.4 8.5 1.0 HE1 A:HIS182 3.4 8.9 1.0 ZN A:ZN303 3.4 7.5 1.0 O A:HOH1002 3.8 9.7 1.0 HD1 A:HIS216 3.8 8.2 1.0 ND2 A:ASN107 4.0 9.2 1.0 HD21 A:ASN107 4.1 11.0 1.0 CE1 A:HIS216 4.1 7.1 1.0 OE2 A:GLU261 4.1 8.8 1.0 CG A:HIS109 4.1 9.0 1.0 ND1 A:HIS109 4.2 10.2 1.0 ND1 A:HIS69 4.2 8.5 1.0 CG A:HIS69 4.2 8.3 1.0 ND1 A:HIS216 4.2 6.8 1.0 CE1 A:HIS182 4.3 7.4 1.0 CG A:GLU145 4.3 7.9 1.0 HB3 A:GLU145 4.4 9.7 1.0 O A:HOH1347 4.4 39.4 1.0 O A:HOH1354 4.5 45.5 1.0 HB2 A:GLU145 4.7 9.7 1.0 CB A:GLU145 4.7 8.0 1.0 OE1 A:GLU261 4.7 7.2 1.0 HG2 A:GLU145 4.8 9.5 1.0 HG3 A:GLU145 4.9 9.5 1.0 CD A:GLU261 4.9 7.0 1.0 O A:HOH1148 4.9 29.7 1.0 HD1 A:HIS69 4.9 10.2 1.0 HD1 A:HIS109 5.0 12.2 1.0

Zinc binding site 2 out of 3 in the High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.4 occ:1.00 NE2 A:HIS231 2.0 7.9 1.0 NE2 A:HIS182 2.0 7.5 1.0 O A:HOH1002 2.0 9.7 1.0 OD1 A:ASP229 2.2 22.2 1.0 OD2 A:ASP229 2.3 15.9 1.0 O A:HOH1246 2.4 28.5 1.0 CG A:ASP229 2.6 13.9 1.0 CE1 A:HIS231 3.0 8.5 1.0 CE1 A:HIS182 3.0 7.4 1.0 CD2 A:HIS231 3.0 8.5 1.0 CD2 A:HIS182 3.0 7.7 1.0 HE1 A:HIS231 3.2 10.2 1.0 HE1 A:HIS182 3.2 8.9 1.0 HD2 A:HIS182 3.2 9.2 1.0 HD2 A:HIS231 3.2 10.2 1.0 CB A:ASP229 4.1 10.3 1.0 ND1 A:HIS231 4.1 8.7 1.0 OD1 A:ASP179 4.2 6.8 1.0 ND1 A:HIS182 4.2 7.5 1.0 CG A:HIS231 4.2 8.0 1.0 CG A:HIS182 4.2 7.3 1.0 O A:HOH1001 4.2 7.7 1.0 O A:HOH1193 4.3 27.3 1.0 HE1 A:HIS109 4.3 11.7 1.0 HB2 A:ASP229 4.4 12.4 1.0 O A:HOH1007 4.5 12.3 1.0 HB3 A:ASP229 4.5 12.4 1.0 ZN A:ZN303 4.7 7.5 1.0 O A:HOH1341 4.8 54.6 1.0 HA A:ASP229 4.8 11.5 1.0 HB3 A:CYS181 4.8 8.7 1.0 CG A:ASP179 4.9 6.7 1.0 HD1 A:HIS231 4.9 10.4 1.0 HD21 A:ASN218 4.9 8.7 1.0 CA A:ASP229 4.9 9.6 1.0 OE1 A:GLU261 4.9 7.2 1.0 HD1 A:HIS182 4.9 9.0 1.0

Zinc binding site 3 out of 3 in the High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High-Resolution Crystal Structure of the Escherichia Coli Dna Repair Enzyme Endonuclease IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:7.5 occ:1.00 HD1 A:HIS216 1.2 8.2 1.0 OD1 A:ASP179 2.0 6.8 1.0 O A:HOH1001 2.0 7.7 1.0 ND1 A:HIS216 2.1 6.8 1.0 OE1 A:GLU145 2.1 7.7 1.0 OE1 A:GLU261 2.2 7.2 1.0 HB2 A:ASP179 3.0 8.2 1.0 CD A:GLU145 3.0 7.1 1.0 CE1 A:HIS216 3.0 7.1 1.0 CD A:GLU261 3.0 7.0 1.0 CG A:ASP179 3.1 6.7 1.0 CG A:HIS216 3.1 6.8 1.0 HE1 A:HIS216 3.2 8.5 1.0 HB2 A:HIS216 3.2 8.5 1.0 OE2 A:GLU261 3.2 8.8 1.0 HB3 A:HIS216 3.3 8.5 1.0 HE1 A:HIS182 3.3 8.9 1.0 OE2 A:GLU145 3.4 7.7 1.0 ZN A:ZN301 3.4 8.3 1.0 CB A:HIS216 3.4 7.1 1.0 HD22 A:ASN218 3.5 8.7 1.0 CB A:ASP179 3.5 6.8 1.0 CE1 A:HIS182 3.7 7.4 1.0 HD21 A:ASN218 4.0 8.7 1.0 O A:HOH1002 4.0 9.7 1.0 HB3 A:ASP179 4.0 8.2 1.0 HE1 A:HIS231 4.0 10.2 1.0 ND2 A:ASN218 4.1 7.2 1.0 NE2 A:HIS182 4.1 7.5 1.0 OD2 A:ASP179 4.2 7.3 1.0 NE2 A:HIS216 4.2 7.6 1.0 CD2 A:HIS216 4.2 7.3 1.0 ND1 A:HIS182 4.2 7.5 1.0 CG A:GLU145 4.3 7.9 1.0 HG3 A:GLU145 4.3 9.5 1.0 HD1 A:HIS182 4.4 9.0 1.0 CG A:GLU261 4.4 7.6 1.0 HG2 A:GLU145 4.5 9.5 1.0 HG3 A:GLU261 4.6 9.1 1.0 CE1 A:HIS231 4.7 8.5 1.0 ZN A:ZN302 4.7 8.4 1.0 HB2 A:GLU261 4.7 8.9 1.0 HA A:ASP179 4.7 8.1 1.0 HD2 A:HIS69 4.7 9.4 1.0 NE2 A:HIS109 4.7 8.2 1.0 CA A:ASP179 4.8 6.8 1.0 HD22 A:ASN107 4.8 11.0 1.0 NE2 A:HIS69 4.9 8.0 1.0 NE2 A:HIS231 4.9 7.9 1.0 CA A:HIS216 4.9 6.6 1.0 CD2 A:HIS182 5.0 7.7 1.0

D.J.Hosfield, Y.Guan, B.J.Haas, R.P.Cunningham, J.A.Tainer. Structure of the Dna Repair Enzyme Endonuclease IV and Its Dna Complex: Double-Nucleotide Flipping at Abasic Sites and Three-Metal-Ion Catalysis. Cell(Cambridge,Mass.) V. 98 397 1999.
ISSN: ISSN 0092-8674
PubMed: 10458614
DOI: 10.1016/S0092-8674(00)81968-6